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Loyal Andrew Goff, Ph.D.


Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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  1. Stein-O'Brien GL, Clark BS, Sherman T, Zibetti C, Hu Q, Sealfon R, Liu S, Qian J, Colantuoni C, Blackshaw S, Goff LA, Fertig EJ. Decomposing Cell Identity for Transfer Learning across Cellular Measurements, Platforms, Tissues, and Species. Cell Syst. 2021 Feb 17; 12(2):203. PMID: 33600760.
    Citations:    Fields:    
  2. Harman CCD, Bailis W, Zhao J, Hill L, Qu R, Jackson RP, Shyer JA, Steach HR, Kluger Y, Goff LA, Rinn JL, Williams A, Henao-Mejia J, Flavell RA. An in vivo screen of noncoding loci reveals that Daedalus is a gatekeeper of an Ikaros-dependent checkpoint during haematopoiesis. Proc Natl Acad Sci U S A. 2021 01 19; 118(3). PMID: 33446502.
    Citations:    Fields:    
  3. Yamaguchi K, Soares AO, Goff LA, Talasila A, Choi JA, Ivenitsky D, Karma S, Brophy B, Devine SE, Meltzer SJ, Kazazian HH. Striking heterogeneity of somatic L1 retrotransposition in single normal and cancerous gastrointestinal cells. Proc Natl Acad Sci U S A. 2020 12 22; 117(51):32215-32222. PMID: 33277430.
    Citations:    Fields:    Translation:HumansCells
  4. Lewis EM, Stein-O'Brien GL, Patino AV, Nardou R, Grossman CD, Brown M, Bangamwabo B, Ndiaye N, Giovinazzo D, Dardani I, Jiang C, Goff LA, Dölen G. Parallel Social Information Processing Circuits Are Differentially Impacted in Autism. Neuron. 2020 11 25; 108(4):659-675.e6. PMID: 33113347.
    Citations:    Fields:    Translation:AnimalsCells
  5. Rattner A, Terrillion CE, Jou C, Kleven T, Hu SF, Williams J, Hou Z, Aggarwal M, Mori S, Shin G, Goff LA, Witter MP, Pletnikov M, Fenton AA, Nathans J. Developmental, cellular, and behavioral phenotypes in a mouse model of congenital hypoplasia of the dentate gyrus. Elife. 2020 10 21; 9. PMID: 33084572.
    Citations:    Fields:    Translation:Animals
  6. Soto-Beasley AI, Walton RL, Valentino RR, Hook PW, Labbé C, Heckman MG, Johnson PW, Goff LA, Uitti RJ, McLean PJ, Springer W, McCallion AS, Wszolek ZK, Ross OA. Screening non-MAPT genes of the Chr17q21 H1 haplotype in Parkinson's disease. Parkinsonism Relat Disord. 2020 09; 78:138-144. PMID: 32829096.
    Citations: 1     Fields:    
  7. Sharma G, Colantuoni C, Goff LA, Fertig EJ, Stein-O'Brien G. projectR: an R/Bioconductor package for transfer learning via PCA, NMF, correlation and clustering. Bioinformatics. 2020 06 01; 36(11):3592-3593. PMID: 32167521.
    Citations: 3     Fields:    
  8. Lu Y, Shiau F, Yi W, Lu S, Wu Q, Pearson JD, Kallman A, Zhong S, Hoang T, Zuo Z, Zhao F, Zhang M, Tsai N, Zhuo Y, He S, Zhang J, Stein-O'Brien GL, Sherman TD, Duan X, Fertig EJ, Goff LA, Zack DJ, Handa JT, Xue T, Bremner R, Blackshaw S, Wang X, Clark BS. Single-Cell Analysis of Human Retina Identifies Evolutionarily Conserved and Species-Specific Mechanisms Controlling Development. Dev Cell. 2020 05 18; 53(4):473-491.e9. PMID: 32386599.
    Citations: 10     Fields:    Translation:HumansAnimalsCells
  9. Friesen M, Warren CR, Yu H, Toyohara T, Ding Q, Florido MHC, Sayre C, Pope BD, Goff LA, Rinn JL, Cowan CA. Mitoregulin Controls ß-Oxidation in Human and Mouse Adipocytes. Stem Cell Reports. 2020 04 14; 14(4):590-602. PMID: 32243843.
    Citations:    Fields:    Translation:HumansAnimalsCells
  10. Lam AN, Aksit MA, Vecchio-Pagan B, Shelton CA, Osorio DL, Anzmann AF, Goff LA, Whitcomb DC, Blackman SM, Cutting GR. Increased expression of anion transporter SLC26A9 delays diabetes onset in cystic fibrosis. J Clin Invest. 2020 01 02; 130(1):272-286. PMID: 31581148.
    Citations: 5     Fields:    Translation:HumansCells
  11. Heng JS, Hackett SF, Stein-O'Brien GL, Winer BL, Williams J, Goff LA, Nathans J. Comprehensive analysis of a mouse model of spontaneous uveoretinitis using single-cell RNA sequencing. Proc Natl Acad Sci U S A. 2019 Dec 16. PMID: 31843893.
    Citations: 2     Fields:    
  12. Carosso GA, Boukas L, Augustin JJ, Nguyen HN, Winer BL, Cannon GH, Robertson JD, Zhang L, Hansen KD, Goff LA, Bjornsson HT. Precocious neuronal differentiation and disrupted oxygen responses in Kabuki syndrome. JCI Insight. 2019 10 17; 4(20). PMID: 31465303.
    Citations: 9     Fields:    Translation:HumansAnimalsCells
  13. Myint L, Wang R, Boukas L, Hansen KD, Goff LA, Avramopoulos D. A screen of 1,049 schizophrenia and 30 Alzheimer's-associated variants for regulatory potential. Am J Med Genet B Neuropsychiatr Genet. 2020 01; 183(1):61-73. PMID: 31503409.
    Citations: 3     Fields:    Translation:HumansCells
  14. Davis-Marcisak EF, Sherman TD, Orugunta P, Stein-O'Brien GL, Puram SV, Roussos Torres ET, Hopkins AC, Jaffee EM, Favorov AV, Afsari B, Goff LA, Fertig EJ. Differential Variation Analysis Enables Detection of Tumor Heterogeneity Using Single-Cell RNA-Sequencing Data. Cancer Res. 2019 10 01; 79(19):5102-5112. PMID: 31337651.
    Citations: 4     Fields:    Translation:Humans
  15. Stein-O'Brien GL, Clark BS, Sherman T, Zibetti C, Hu Q, Sealfon R, Liu S, Qian J, Colantuoni C, Blackshaw S, Goff LA, Fertig EJ. Decomposing Cell Identity for Transfer Learning across Cellular Measurements, Platforms, Tissues, and Species. Cell Syst. 2019 05 22; 8(5):395-411.e8. PMID: 31121116.
    Citations: 27     Fields:    Translation:HumansAnimalsCells
  16. Clark BS, Stein-O'Brien GL, Shiau F, Cannon GH, Davis-Marcisak E, Sherman T, Santiago CP, Hoang TV, Rajaii F, James-Esposito RE, Gronostajski RM, Fertig EJ, Goff LA, Blackshaw S. Single-Cell RNA-Seq Analysis of Retinal Development Identifies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specification. Neuron. 2019 06 19; 102(6):1111-1126.e5. PMID: 31128945.
    Citations: 52     Fields:    Translation:AnimalsCells
  17. Heng JS, Rattner A, Stein-O'Brien GL, Winer BL, Jones BW, Vernon HJ, Goff LA, Nathans J. Hypoxia tolerance in the Norrin-deficient retina and the chronically hypoxic brain studied at single-cell resolution. Proc Natl Acad Sci U S A. 2019 04 30; 116(18):9103-9114. PMID: 30988181.
    Citations: 11     Fields:    Translation:AnimalsCells
  18. Myint L, Avramopoulos DG, Goff LA, Hansen KD. Linear models enable powerful differential activity analysis in massively parallel reporter assays. BMC Genomics. 2019 Mar 12; 20(1):209. PMID: 30866806.
    Citations: 7     Fields:    Translation:Humans
  19. Sabbagh MF, Heng JS, Luo C, Castanon RG, Nery JR, Rattner A, Goff LA, Ecker JR, Nathans J. Transcriptional and epigenomic landscapes of CNS and non-CNS vascular endothelial cells. Elife. 2018 09 06; 7. PMID: 30188322.
    Citations: 48     Fields:    Translation:AnimalsCells
  20. Stein-O'Brien GL, Arora R, Culhane AC, Favorov AV, Garmire LX, Greene CS, Goff LA, Li Y, Ngom A, Ochs MF, Xu Y, Fertig EJ. Enter the Matrix: Factorization Uncovers Knowledge from Omics. Trends Genet. 2018 10; 34(10):790-805. PMID: 30143323.
    Citations: 26     Fields:    Translation:Humans
  21. Hook PW, McClymont SA, Cannon GH, Law WD, Morton AJ, Goff LA, McCallion AS. Single-Cell RNA-Seq of Mouse Dopaminergic Neurons Informs Candidate Gene Selection for Sporadic Parkinson Disease. Am J Hum Genet. 2018 03 01; 102(3):427-446. PMID: 29499164.
    Citations: 17     Fields:    Translation:AnimalsCells
  22. Chevée M, Robertson JJ, Cannon GH, Brown SP, Goff LA. Variation in Activity State, Axonal Projection, and Position Define the Transcriptional Identity of Individual Neocortical Projection Neurons. Cell Rep. 2018 01 09; 22(2):441-455. PMID: 29320739.
    Citations: 21     Fields:    Translation:Cells
  23. Mowel WK, McCright SJ, Kotzin JJ, Collet MA, Uyar A, Chen X, DeLaney A, Spencer SP, Virtue AT, Yang E, Villarino A, Kurachi M, Dunagin MC, Pritchard GH, Stein J, Hughes C, Fonseca-Pereira D, Veiga-Fernandes H, Raj A, Kambayashi T, Brodsky IE, O'Shea JJ, Wherry EJ, Goff LA, Rinn JL, Williams A, Flavell RA, Henao-Mejia J. Group 1 Innate Lymphoid Cell Lineage Identity Is Determined by a cis-Regulatory Element Marked by a Long Non-coding RNA. Immunity. 2017 09 19; 47(3):435-449.e8. PMID: 28930659.
    Citations: 12     Fields:    Translation:AnimalsCells
  24. Kim J, Hughes EG, Shetty AS, Arlotta P, Goff LA, Bergles DE, Brown SP. Changes in the Excitability of Neocortical Neurons in a Mouse Model of Amyotrophic Lateral Sclerosis Are Not Specific to Corticospinal Neurons and Are Modulated by Advancing Disease. J Neurosci. 2017 09 13; 37(37):9037-9053. PMID: 28821643.
    Citations: 24     Fields:    Translation:AnimalsCells
  25. Benjamin JS, Pilarowski GO, Carosso GA, Zhang L, Huso DL, Goff LA, Vernon HJ, Hansen KD, Bjornsson HT. A ketogenic diet rescues hippocampal memory defects in a mouse model of Kabuki syndrome. Proc Natl Acad Sci U S A. 2017 01 03; 114(1):125-130. PMID: 27999180.
    Citations: 21     Fields:    Translation:Animals
  26. Kotzin JJ, Spencer SP, McCright SJ, Kumar DBU, Collet MA, Mowel WK, Elliott EN, Uyar A, Makiya MA, Dunagin MC, Harman CCD, Virtue AT, Zhu S, Bailis W, Stein J, Hughes C, Raj A, Wherry EJ, Goff LA, Klion AD, Rinn JL, Williams A, Flavell RA, Henao-Mejia J. The long non-coding RNA Morrbid regulates Bim and short-lived myeloid cell lifespan. Nature. 2016 09 08; 537(7619):239-243. PMID: 27525555.
    Citations: 82     Fields:    Translation:HumansAnimalsCells
  27. Feyder M, Goff LA. Investigating long noncoding RNAs using animal models. J Clin Invest. 2016 08 01; 126(8):2783-91. PMID: 27479747.
    Citations: 7     Fields:    Translation:HumansAnimalsCells
  28. Hart RP, Goff LA. Long noncoding RNAs: Central to nervous system development. Int J Dev Neurosci. 2016 Dec; 55:109-116. PMID: 27296516.
    Citations: 13     Fields:    Translation:HumansAnimals
  29. Gottschalk LB, Vecchio-Pagan B, Sharma N, Han ST, Franca A, Wohler ES, Batista DA, Goff LA, Cutting GR. Creation and characterization of an airway epithelial cell line for stable expression of CFTR variants. J Cyst Fibros. 2016 05; 15(3):285-94. PMID: 26694805.
    Citations: 11     Fields:    Translation:HumansCells
  30. Goff LA, Rinn JL. Linking RNA biology to lncRNAs. Genome Res. 2015 Oct; 25(10):1456-65. PMID: 26430155.
    Citations: 73     Fields:    Translation:HumansAnimalsCells
  31. Goff LA, Groff AF, Sauvageau M, Trayes-Gibson Z, Sanchez-Gomez DB, Morse M, Martin RD, Elcavage LE, Liapis SC, Gonzalez-Celeiro M, Plana O, Li E, Gerhardinger C, Tomassy GS, Arlotta P, Rinn JL. Spatiotemporal expression and transcriptional perturbations by long noncoding RNAs in the mouse brain. Proc Natl Acad Sci U S A. 2015 Jun 02; 112(22):6855-62. PMID: 26034286.
    Citations: 56     Fields:    Translation:AnimalsCells
  32. Molyneaux BJ, Goff LA, Brettler AC, Chen HH, Hrvatin S, Rinn JL, Arlotta P. DeCoN: genome-wide analysis of in vivo transcriptional dynamics during pyramidal neuron fate selection in neocortex. Neuron. 2015 Jan 21; 85(2):275-288. PMID: 25556833.
    Citations: 94     Fields:    Translation:AnimalsCells
  33. Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L. Corrigendum: Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 2014 Oct; 9(10):2513. PMID: 25255093.
  34. Lodato S, Molyneaux BJ, Zuccaro E, Goff LA, Chen HH, Yuan W, Meleski A, Takahashi E, Mahony S, Rinn JL, Gifford DK, Arlotta P. Gene co-regulation by Fezf2 selects neurotransmitter identity and connectivity of corticospinal neurons. Nat Neurosci. 2014 Aug; 17(8):1046-54. PMID: 24997765.
    Citations: 37     Fields:    Translation:AnimalsCells
  35. Davila JL, Goff LA, Ricupero CL, Camarillo C, Oni EN, Swerdel MR, Toro-Ramos AJ, Li J, Hart RP. A positive feedback mechanism that regulates expression of miR-9 during neurogenesis. PLoS One. 2014; 9(4):e94348. PMID: 24714615.
    Citations: 12     Fields:    Translation:AnimalsCells
  36. Hacisuleyman E, Goff LA, Trapnell C, Williams A, Henao-Mejia J, Sun L, McClanahan P, Hendrickson DG, Sauvageau M, Kelley DR, Morse M, Engreitz J, Lander ES, Guttman M, Lodish HF, Flavell R, Raj A, Rinn JL. Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre. Nat Struct Mol Biol. 2014 Feb; 21(2):198-206. PMID: 24463464.
    Citations: 236     Fields:    Translation:HumansAnimalsCells
  37. Silverman IM, Li F, Alexander A, Goff L, Trapnell C, Rinn JL, Gregory BD. RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome. Genome Biol. 2014 Jan 07; 15(1):R3. PMID: 24393486.
    Citations: 32     Fields:    Translation:HumansCells
  38. Sauvageau M, Goff LA, Lodato S, Bonev B, Groff AF, Gerhardinger C, Sanchez-Gomez DB, Hacisuleyman E, Li E, Spence M, Liapis SC, Mallard W, Morse M, Swerdel MR, D'Ecclessis MF, Moore JC, Lai V, Gong G, Yancopoulos GD, Frendewey D, Kellis M, Hart RP, Valenzuela DM, Arlotta P, Rinn JL. Multiple knockout mouse models reveal lincRNAs are required for life and brain development. Elife. 2013 Dec 31; 2:e01749. PMID: 24381249.
    Citations: 304     Fields:    Translation:Animals
  39. Goff LA, Rinn JL. Poly-combing the genome for RNA. Nat Struct Mol Biol. 2013 Dec; 20(12):1344-6. PMID: 24304912.
    Citations: 3     Fields:    Translation:HumansAnimalsCells
  40. Di Ruscio A, Ebralidze AK, Benoukraf T, Amabile G, Goff LA, Terragni J, Figueroa ME, De Figueiredo Pontes LL, Alberich-Jorda M, Zhang P, Wu M, D'Alò F, Melnick A, Leone G, Ebralidze KK, Pradhan S, Rinn JL, Tenen DG. DNMT1-interacting RNAs block gene-specific DNA methylation. Nature. 2013 Nov 21; 503(7476):371-6. PMID: 24107992.
    Citations: 196     Fields:    Translation:HumansCells
  41. Henao-Mejia J, Williams A, Goff LA, Staron M, Licona-Limón P, Kaech SM, Nakayama M, Rinn JL, Flavell RA. The microRNA miR-181 is a critical cellular metabolic rheostat essential for NKT cell ontogenesis and lymphocyte development and homeostasis. Immunity. 2013 May 23; 38(5):984-97. PMID: 23623381.
    Citations: 111     Fields:    Translation:AnimalsCells
  42. Sun L, Goff LA, Trapnell C, Alexander R, Lo KA, Hacisuleyman E, Sauvageau M, Tazon-Vega B, Kelley DR, Hendrickson DG, Yuan B, Kellis M, Lodish HF, Rinn JL. Long noncoding RNAs regulate adipogenesis. Proc Natl Acad Sci U S A. 2013 Feb 26; 110(9):3387-92. PMID: 23401553.
    Citations: 152     Fields:    Translation:AnimalsCells
  43. Trapnell C, Hendrickson DG, Sauvageau M, Goff L, Rinn JL, Pachter L. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat Biotechnol. 2013 Jan; 31(1):46-53. PMID: 23222703.
    Citations: 1458     Fields:    Translation:HumansCells
  44. Washietl S, Will S, Hendrix DA, Goff LA, Rinn JL, Berger B, Kellis M. Computational analysis of noncoding RNAs. Wiley Interdiscip Rev RNA. 2012 Nov-Dec; 3(6):759-78. PMID: 22991327.
    Citations: 30     Fields:    Translation:HumansAnimalsCells
  45. Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 2012 Mar 01; 7(3):562-78. PMID: 22383036.
    Citations: 4692     Fields:    
  46. Pichardo-Casas I, Goff LA, Swerdel MR, Athie A, Davila J, Ramos-Brossier M, Lapid-Volosin M, Friedman WJ, Hart RP, Vaca L. Expression profiling of synaptic microRNAs from the adult rat brain identifies regional differences and seizure-induced dynamic modulation. Brain Res. 2012 Feb 03; 1436:20-33. PMID: 22197703.
    Citations: 41     Fields:    Translation:AnimalsCells
  47. Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, Rinn JL. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 2011 Sep 15; 25(18):1915-27. PMID: 21890647.
    Citations: 1452     Fields:    Translation:HumansCells
  48. Bail S, Swerdel M, Liu H, Jiao X, Goff LA, Hart RP, Kiledjian M. Differential regulation of microRNA stability. RNA. 2010 May; 16(5):1032-9. PMID: 20348442.
    Citations: 133     Fields:    Translation:HumansCells
  49. Goff LA, Davila J, Swerdel MR, Moore JC, Cohen RI, Wu H, Sun YE, Hart RP. Ago2 immunoprecipitation identifies predicted microRNAs in human embryonic stem cells and neural precursors. PLoS One. 2009 Sep 28; 4(9):e7192. PMID: 19784364.
    Citations: 66     Fields:    Translation:HumansCells
  50. Chang YW, Goff LA, Li H, Kane-Goldsmith N, Tzatzalos E, Hart RP, Young W, Grumet M. Rapid induction of genes associated with tissue protection and neural development in contused adult spinal cord after radial glial cell transplantation. J Neurotrauma. 2009 Jul; 26(7):979-93. PMID: 19257808.
    Citations: 8     Fields:    Translation:AnimalsCells
  51. Li H, Han YR, Bi C, Davila J, Goff LA, Thompson K, Swerdel M, Camarillo C, Ricupero CL, Hart RP, Plummer MR, Grumet M. Functional differentiation of a clone resembling embryonic cortical interneuron progenitors. Dev Neurobiol. 2008 Dec; 68(14):1549-64. PMID: 18814314.
    Citations: 8     Fields:    Translation:AnimalsCells
  52. Goff LA, Boucher S, Ricupero CL, Fenstermacher S, Swerdel M, Chase LG, Adams CC, Chesnut J, Lakshmipathy U, Hart RP. Differentiating human multipotent mesenchymal stromal cells regulate microRNAs: prediction of microRNA regulation by PDGF during osteogenesis. Exp Hematol. 2008 Oct; 36(10):1354-1369. PMID: 18657893.
    Citations: 23     Fields:    Translation:HumansCells
  53. Lakshmipathy U, Love B, Goff LA, Jörnsten R, Graichen R, Hart RP, Chesnut JD. MicroRNA expression pattern of undifferentiated and differentiated human embryonic stem cells. Stem Cells Dev. 2007 Dec; 16(6):1003-16. PMID: 18004940.
    Citations: 66     Fields:    Translation:HumansCells
  54. Goff LA, Davila J, Jörnsten R, Keles S, Hart RP. Bioinformatic analysis of neural stem cell differentiation. J Biomol Tech. 2007 Sep; 18(4):205-12. PMID: 17916793.
    Citations: 3     Fields:    Translation:HumansAnimalsCells
  55. Goff LA, Yang M, Bowers J, Getts RC, Padgett RW, Hart RP. Rational probe optimization and enhanced detection strategy for microRNAs using microarrays. RNA Biol. 2005 Jul-Sep; 2(3):93-100. PMID: 17114923.
    Citations: 18     Fields:    Translation:AnimalsCells
  56. Goff LA, Bowers J, Schwalm J, Howerton K, Getts RC, Hart RP. Evaluation of sense-strand mRNA amplification by comparative quantitative PCR. BMC Genomics. 2004 Oct 06; 5:76. PMID: 15469607.
    Citations: 19     Fields:    Translation:Animals
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.